We know, that $\mathbf{Hom}(\mathcal{F},\mathcal{G})$ is abelian group of all morphisms between $\mathcal{O}_X$-modules $\mathcal{F}$ and $\mathcal{G}$, and $\mathcal{Hom}(\mathcal{F},\mathcal{G})$ is sheaf, which section $\mathcal{Hom}(\mathcal{F},\mathcal{G})(U)$ is $\mathcal{O}_X(U)$-module of all morphisms between module $\mathcal{F}(U)$ and module $\mathcal{G}(U)$.
So, for me statement $\Gamma(\mathcal{Hom}(\mathcal{F},\mathcal{G}))=\mathbf{Hom}(\mathcal{F},\mathcal{G})$ sounds like "every morphism between two $\mathcal{O}_X$-modules uniquely determined by morphism between global sections of them". It can't be true, right? So, where is mistake?